fMRIPrep illegal slice timing value for Merlin data

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I’m trying to run data from SherlockMerlin through the latest version of fMRIPrep and am running into an issue because one of the values for slice timing is 1.50003 which is slightly larger than the TR time which is 1.5. Does anyone know what this sort of problem might be coming from and the best way to fix? I’m guessing simply editing the value to be 1.5 is not advised?

The error I receive:

Standard error:
++ 3dTshift: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit]
^[[7m*+ WARNING:^[[0m   If you are performing spatial transformations on an oblique dset,
  such as /scratch/Fri/jsmentch/cache/fmriprep_wf/single_subject_19_wf/func_preproc_task_MerlinMovie_wf/bold_stc_wf/slice_timing_\
correction/sub-19_task-MerlinMovie_bold.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
     3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/scratch/Fri/jsmentch/cache/fmriprep_wf/single_subject_19_wf/func_preproc_task_MerlinMovie_wf/bold_stc_wf/slic\
e_timing_correction/sub-19_task-MerlinMovie_bold.nii.gz is 22.319094 degrees from plumb.
^[[7m** FATAL ERROR:^[[0m Illegal value 1.50003 in tpattern file slice_timing.1D
** Program compile date = Jun 12 2017
Return code: 1
2

It looks like the whole SliceTiming information is given in msec in your case, which violates the BIDS specifications. I think the BIDS-Validator catches this, so please run your dataset through the validator first.

A slice time of 1.5s when your TR is 1.5s is absolutely implausible. If you don’t know how to reconstruct accurate slice timing records in seconds for the dataset, I would recommend skipping the correction altogether with --ignore slicetiming.

1 Like
3

Ah… I see that makes sense that it is in ms, I had already run everything with --ignore slicetiming anyway after not being able to figure this out. I will write a comment on the openneuro page that it appears the slice timing is in ms to document. Thanks!